Knowledge of what genes are (and are not) present in particular varieties is particularly helpful. Breeders can use this information to select the best parents for use in a crossing program, or to add value to an existing population by knowing what genes will be segregating. Product managers and pathologists can use this information to better target varieties to specific regions where resistance genes will be effective, and identify varieties that meet local requirements of grain quality, maturity, etc. The QTL profiles listed here are based on either whole-genome sequencing results, and/or genotyping with mid-density marker platforms using key trait markers as described above.
For many genes, there are well-defined favorable ([+]) and unfavorable ([-]) alleles that can be identified. For others, the situation is more complex with situations such as multiple favorable alleles, alleles that are favorable in some situations but unfavorable in others, allele activity series (low, medium, and high trait value), and many other situations being seen depending on the underlying biology of the genes involved. In these cases, efforts have been made to best communicate the breeding value of the alleles identified in each line.
The frequencies of most genes have also been assessed in the elite indica material used by most breeding programs. The favorable alleles of the majority of genes are either absent (almost 50%) or very rare (15%) in the elite indica material, which makes using the genes in elite population improvement programs challenging. IRRI is working to create elite donor lines for the most valuable genes, thus providing an entry point into the elite breeding process.